kmer counting - meryl - upgraded

assembly-largegenome/galaxy-workflow-kmer-counting

Author(s)
Anna Syme
Version
2
Last updated
May 8, 2024
License
GPL-3.0-or-later
Tags
GTN
LG-WF

Features
Tutorial
Large genome assembly and polishing
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00017
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nIllumina reads R1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Meryl - count kmers"];
  0 -->|output| 1;
  899ddd93-4c0f-4f81-a973-8120494ed983["Output\nMeryl on input dataset(s): read-db.meryldb"];
  1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;
  style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;
  2["Meryl - generate histogram"];
  1 -->|read_db| 2;
  3["Genomescope"];
  2 -->|read_db_hist| 3;
  efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac["Output\nGenomeScope on input dataset(s) Transformed log plot"];
  3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;
  style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;
  701df341-5767-44bc-ade2-6af498ab7467["Output\nGenomeScope on input dataset(s) Transformed linear plot"];
  3 --> 701df341-5767-44bc-ade2-6af498ab7467;
  style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;
  85fa4004-b351-47b3-84aa-6788d338037a["Output\nGenomeScope on input dataset(s) Log plot"];
  3 --> 85fa4004-b351-47b3-84aa-6788d338037a;
  style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;
  c71ce055-98f0-4354-9397-2f8833b90cc4["Output\nGenomeScope on input dataset(s) Linear plot"];
  3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;
  style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Illumina reads R1

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 Meryl Meryl - count kmers
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 Meryl Meryl - generate histogram
toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2 GenomeScope Genomescope

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
5 b74cf5a09 2024-05-07 09:34:21 Update Galaxy-Workflow-kmer_counting.ga
4 e8ddbcdd5 2024-05-01 04:32:16 new versions of workflows
3 0be0483e2 2024-05-01 04:22:46 Rename Galaxy-Workflow-kmer_counting.ga to Galaxy-Workflow-kmer_counting_old.ga
2 62e77944b 2023-02-17 09:53:23 add/complete creator info on workflows
1 9fcb3aeec 2022-10-07 06:24:16 large genome tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows